In the past, with my '99 GC, I carried my canoe with foam carriers and ratchet straps that would wrap around the raised roof rails and hook back onto themselves. With the flush mount rails on the new '12, I can't do that. And I don't really like the look of driving around with cross bars mounted all the time. Has anyone come up with a solution for hooking straps/bungees to the flush mount rails? I'm thinking some sort of mount that fits into the flush rails and provides an eye hook. Thoughts?

Looking at the rails, I'd think that would be easy to rig up during a trip to your local hardware store. You'd need a plate that fits inside the rail, another that fits on top of the rail, and an eyebolt and nut to cinch it all together on the rail. How hard could that be?

I bought the Mopar crossbars from my Jeep dealer for $212, but won't have a reason to even take them out of the box until next Spring.

Sounds easy enough, except for the fact that as I'm visualizing your solution, the nut is down inside the rail track underneath the plate. Not sure how to cinch everything down if I can't get access to that nut. I suppose I could have someone tack weld the nut to the plate?

Two years ago, I made a Cedar Strip Canoe and wanted something a little more reliable / dependable on the roof than blocks of foam and rope.
So I sprang for the Mopar crossbars and the Canoe Kit to fit my Pacifica. I believe they are both made by Thule.
They come on and off quite easily.
They are excellent quality and really hold the canoe tight to the roof. They also came with black straps to hold it to the racks, but I augment that with blue adjustable straps front and back.

Now I'm hoping the crossbars that I bought for my Pacifica also fit the GC.
Here is a pic:

+1, I wouldn't recommend putting a load of that weight or that much air resistance up top without a proper set of crossbars. It looks too easy to cause damage to the roof of a vehicle or expensive gear. Worse, it could result in lost equipment and chaos on the highway. Maybe the raised rails on the '99 JGC allowed you to get better purchase, but the WK2 rails are pretty flimsy to start.

Thanks, all. I guess I will bite the bullet and get the Thule rack. I just have to figure out if I'm going to leave the cross bars on or take them off between uses. I don't like the look of them on when not carrying a load, but I also don't know where I would stash them in the Jeep so that I was ready to carry a load if necessary.

I agree - with the wind noise you won't want to leave it up all the time, regardless of how it looks.

If my old rack fits, I'll put it on and take a better pic of it.

Another trick I picked up from some canoeing friends of mine was to make up 2 special short straps (out of seat-belt material) that bolt under the hood at two front corner locations.
They sit folded under the hood when not needed, but when required slip between the fender and hood and provide a neat place to anchor your front two straps
(without chafing the front edge of the hood).
I'll post a pic of them in my new JC after I transfer them over.